The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks

Abstract

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

Figure 1.

Venn diagram showing the number of shared taxa at genus level between SILVA, RDP-II and Greengenes. Only taxa containing sequences from cultivated organisms are included in this comparison. The overlapping part in the middle shows the number of all taxa jointly shared by all three databases; the other overlaps show taxa shared between two databases, but not the third. RDP-II and Greengenes share no other taxa in addition to the 949 shared jointly by all three databases.